Would you consider houses of worship near the subject property to be external obsolescence?
It is quite possible that anything not on the subject property — including a house of worship — could cause external obsolescence. Excess noise, traffic and other issues might ensue. It is up to you as the appraiser to assess whether or not these conditions exist and if they cause external obsolescence.
Subject is a purchase marketed as 3,100 sq.ft. County has subject listed as 2,059 sq.ft. Appears subject possesses a finished upper level, apparently original and legal, which does not possess a bathroom.
I presume, at a minimum, that there is functional obsolescence? However, presuming the upper level is legally finished and otherwise of good quality, it's hard to compare to other properties with 3,000 sq.ft. that offer greater utility. Would you give partial value to upper level and not include in sq ft calculations?
It is not possible for me to give advice about specific properties. However, here are some thoughts that may be helpful. It is up to you to determine what the actual GLA is and use it as a basis for your appraisal. This is a separate problem from estimating what the value is. From what you say I see no reason not to include the upper area in the GLA. However you can give it less value than other parts of the house. You must make this judgment based on what is expected in your market area. You must describe what is causing a loss of value (if any) due to functional obsolescence.